Crux glossary

Mass spectrometry terminology

c-term peptide: The last peptide in the protein,
occurring at the c-terminal end of the protein.

decoy peptide: A shuffled, reversed or randomly
generated peptide sequence. Matches to decoy peptides are used
for two purposes: to estimate statistical confidence measures
such as the false discovery rate, and to train machine learning
methods to recognize correctly identified spectra.

modification: A chemical modification of a single amino
acid, typically corresponding to the addition of a molecular
group to the amino acid side chain.

n-term peptide: The first peptide in the protein,
occurring at the n-terminal end of the protein.

peptide: A subsequence of a protein.

peptide-spectrum match (PSM): An observed spectrum
paired with a peptide sequence, along with a score quantifying
the quality of the match.

static modification: A chemical modification of a
single amino that is expected to occur on every instance of that
amino acid. A common example is carbamidomethylation of
cysteine, which adds 57.02146 Da to the mass of every
cysteine.

target peptide: A real peptide, usually drawn from a
protein database.

trypsin: An enzyme used to cleave a protein into
peptides.

variable modification: A chemical modification of a
single amino that is expected to occur on some instances of that
amino acid but not others. A common example is phosphorylation
of serine, threonine or tyrosine, which adds a mass of 79.966331
Da to each of those amino acids.

Analysis terminology

false discovery rate (FDR): Estimated proportion of
incorrectly identifications among a set of PSMs, peptides or
proteins.

support vector machine (SVM): A machine learning method
that learns to classify data objects into two groups.